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protocols::flxbb::LayerDesignOperation Class Reference

#include <LayerDesignOperation.hh>

Inheritance diagram for protocols::flxbb::LayerDesignOperation:
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Collaboration diagram for protocols::flxbb::LayerDesignOperation:
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Public Types

typedef std::string String
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef
core::pack::task::PackerTask 
PackerTask
 
typedef
core::pack::task::operation::TaskOperation 
TaskOperation
 
typedef
core::pack::task::operation::TaskOperationOP 
TaskOperationOP
 
typedef TaskOperation parent
 
typedef utility::tag::TagPtr TagPtr
 
typedef std::map< std::string,
TaskOperationOP
TaskLayers
 
typedef std::pair< std::string,
TaskOperationOP
TaskLayer
 
typedef std::map< std::string,
std::string > 
LayerDefinitions
 
typedef std::pair< std::string,
std::string > 
LayerDefinition
 
typedef std::map< std::string,
LayerDefinitions
LayerResidues
 
typedef std::pair< std::string,
LayerDefinitions
Layer
 
- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr TagPtr
 
typedef pose::Pose Pose
 

Public Member Functions

 LayerDesignOperation ()
 default constructor More...
 
 LayerDesignOperation (bool dsgn_core, bool dsgn_boundary, bool dsgn_surface)
 value constructor More...
 
virtual ~LayerDesignOperation ()
 destructor More...
 
virtual TaskOperationOP clone () const
 make clone More...
 
void design_layer (bool const dsgn_core, bool const dsgn_boundary, bool const dsgn_surface)
 layer to be designed More...
 
void sasa_surface (Real const r, String const ss="")
 accessible surface for evaluating residues are in surface or not More...
 
void sasa_core (Real const r, String const ss="")
 accessible surface for evaluating residues are in core or not More...
 
void pore_radius (Real ps)
 set pore radius for colculating asa More...
 
void set_verbose (bool const b)
 set verbose More...
 
void set_restrict_restypes (bool const b)
 set restrict_restypes More...
 
void use_original_seq ()
 use original sequence for not designed layer More...
 
void make_pymol_script (bool value)
 make pymol scripts showing the different layers More...
 
void parse_tag (TagPtr tag)
 Used to parse an xml-like tag to load parameters and properties. More...
 
virtual void apply (Pose const &pose, PackerTask &task) const
 apply More...
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual ~TaskOperation ()
 
virtual void parse_def (utility::lua::LuaObject const &def)
 

Private Member Functions

utility::vector1< boolget_restrictions (std::string const &layer, std::string const &default_layer, std::string const &ss_type) const
 
void set_default_layer_residues ()
 
std::string pos2select (utility::vector1< Size > const &pos) const
 utility function to transform a vector of position into a pymol selection command More...
 
void write_pymol_script (Pose const &pos, toolbox::SelectResiduesByLayerOP srbl, std::map< std::string, utility::vector1< bool > > const &layer_specification, bool las_ligand, std::string const &filename) const
 write a pymol command with the different layers as selections More...
 

Private Attributes

bool add_helix_capping_
 add helix capping ? More...
 
bool use_original_
 use original sequence for not designed layer ? More...
 
bool repack_non_designed_residues_
 
bool verbose_
 
bool restrict_restypes_
 
bool make_pymol_script_
 
LayerResidues layer_residues_
 
std::map< std::string, booldesign_layer_
 
TaskLayers task_layers_
 
toolbox::SelectResiduesByLayerOP srbl_
 

Member Typedef Documentation

typedef std::pair< std::string, std::string > protocols::flxbb::LayerDesignOperation::LayerDefinition
typedef std::map< std::string, std::string > protocols::flxbb::LayerDesignOperation::LayerDefinitions
typedef utility::tag::TagPtr protocols::flxbb::LayerDesignOperation::TagPtr

Constructor & Destructor Documentation

protocols::flxbb::LayerDesignOperation::LayerDesignOperation ( )

default constructor

References set_default_layer_residues().

Referenced by clone().

protocols::flxbb::LayerDesignOperation::LayerDesignOperation ( bool  dsgn_core,
bool  dsgn_boundary,
bool  dsgn_surface 
)

value constructor

References design_layer(), and set_default_layer_residues().

protocols::flxbb::LayerDesignOperation::~LayerDesignOperation ( )
virtual

destructor

Member Function Documentation

void protocols::flxbb::LayerDesignOperation::apply ( Pose const &  pose,
PackerTask task 
) const
virtual
core::pack::task::operation::TaskOperationOP protocols::flxbb::LayerDesignOperation::clone ( ) const
virtual

make clone

clone

Implements core::pack::task::operation::TaskOperation.

References LayerDesignOperation().

void protocols::flxbb::LayerDesignOperation::design_layer ( bool const  dsgn_core,
bool const  dsgn_boundary,
bool const  dsgn_surface 
)

layer to be designed

References srbl_.

Referenced by LayerDesignOperation().

utility::vector1< bool > protocols::flxbb::LayerDesignOperation::get_restrictions ( std::string const &  layer,
std::string const &  default_layer,
std::string const &  ss_type 
) const
private
void protocols::flxbb::LayerDesignOperation::make_pymol_script ( bool  value)
inline

make pymol scripts showing the different layers

Referenced by parse_tag().

void protocols::flxbb::LayerDesignOperation::parse_tag ( TagPtr  tag)
virtual
void protocols::flxbb::LayerDesignOperation::pore_radius ( Real  ps)

set pore radius for colculating asa

References srbl_.

std::string protocols::flxbb::LayerDesignOperation::pos2select ( utility::vector1< Size > const &  pos) const
private

utility function to transform a vector of position into a pymol selection command

References protocols::kinmatch::str().

Referenced by write_pymol_script().

void protocols::flxbb::LayerDesignOperation::sasa_core ( Real const  r,
String const  ss = "" 
)

accessible surface for evaluating residues are in core or not

References srbl_.

void protocols::flxbb::LayerDesignOperation::sasa_surface ( Real const  r,
String const  ss = "" 
)

accessible surface for evaluating residues are in surface or not

References srbl_.

void protocols::flxbb::LayerDesignOperation::set_default_layer_residues ( )
private
void protocols::flxbb::LayerDesignOperation::set_restrict_restypes ( bool const  b)
inline

set restrict_restypes

References protocols::match::upstream::b.

Referenced by parse_tag().

void protocols::flxbb::LayerDesignOperation::set_verbose ( bool const  b)
inline

set verbose

References protocols::match::upstream::b.

Referenced by parse_tag().

void protocols::flxbb::LayerDesignOperation::use_original_seq ( )
inline

use original sequence for not designed layer

void protocols::flxbb::LayerDesignOperation::write_pymol_script ( Pose const &  pos,
toolbox::SelectResiduesByLayerOP  srbl,
std::map< std::string, utility::vector1< bool > > const &  layer_specification,
bool  las_ligand,
std::string const &  filename 
) const
private

write a pymol command with the different layers as selections

References core::pose::Pose::dump_pdb(), pos2select(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

Member Data Documentation

bool protocols::flxbb::LayerDesignOperation::add_helix_capping_
private

add helix capping ?

Referenced by apply().

std::map< std::string, bool > protocols::flxbb::LayerDesignOperation::design_layer_
private
LayerResidues protocols::flxbb::LayerDesignOperation::layer_residues_
private
bool protocols::flxbb::LayerDesignOperation::make_pymol_script_
private

Referenced by apply().

bool protocols::flxbb::LayerDesignOperation::repack_non_designed_residues_
private

Referenced by apply(), and parse_tag().

bool protocols::flxbb::LayerDesignOperation::restrict_restypes_
private
toolbox::SelectResiduesByLayerOP protocols::flxbb::LayerDesignOperation::srbl_
private
TaskLayers protocols::flxbb::LayerDesignOperation::task_layers_
private

Referenced by apply(), and parse_tag().

bool protocols::flxbb::LayerDesignOperation::use_original_
private

use original sequence for not designed layer ?

Referenced by parse_tag().

bool protocols::flxbb::LayerDesignOperation::verbose_
private

Referenced by apply().


The documentation for this class was generated from the following files: